Plastome Evolution and Codon Usage Dynamics in Argentina (Rosaceae): Phylogenomic Resolution and Adaptive Signatures

The genus Argentina (Rosaceae) exhibits extensive morphological plasticity that has long complicated taxonomic delimitation and phylogenetic inference. Here, we report complete chloroplast genome sequences for three species-A. stenophylla var. stenophylla, A. anserina, and A. leuconota var. leuconota-and integrate them with 15 previously published congeneric plastomes to investigate genome architecture, phylogenetic relationships, and synonymous codon usage bias (CUB). All 18 plastomes retain the canonical quadripartite structure and near-identical gene complements, underscoring extraordinary architectural stability. Phylogenomic reconstruction strongly supports the monophyly of Argentina and resolves five well-supported clades, corroborating the transfer of Sibbaldia micropetala and S. phanerophlebia into Argentina. Codon analysis revealed that the effective number of codons (ENC) is consistently high (~48), while the codon adaptation index (CAI) remains uniformly low (~0.17), together indicating weak overall codon bias. Neutrality, ENC, and PR2 analyses converge to indicate that natural selection-not mutational pressure-is the principal force shaping CUB, accounting for over 95% of observed variation. Although hierarchical clustering of RSCU values largely recapitulates the plastome phylogeny, discrete departures in specific lineages suggest that ecological selection may have independently modulated codon optima. Notably, only two amino acids (Gln and Gly) retain universally conserved optimal codons, whereas seven amino acids exhibit dual optimal codons with pronounced interspecific variation. These findings reveal a decoupled evolutionary architecture: while genome organization is ultraconserved, synonymous sites undergo ongoing selective refinement. This dissociation between rigid genomic architecture and malleable codon configurations might point to a coevolutionary process in which plastid translational machinery and environmental selection reciprocally fine-tune synonymous codon choice, shedding light on how Argentina modulates organellar gene expression to cope with environmental heterogeneity across the Sino-Himalayan region and the Malay Archipelago.